Job ID = 1293417 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,569,486 reads read : 51,138,972 reads written : 51,138,972 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:22:45 25569486 reads; of these: 25569486 (100.00%) were paired; of these: 6158589 (24.09%) aligned concordantly 0 times 13684215 (53.52%) aligned concordantly exactly 1 time 5726682 (22.40%) aligned concordantly >1 times ---- 6158589 pairs aligned concordantly 0 times; of these: 2508171 (40.73%) aligned discordantly 1 time ---- 3650418 pairs aligned 0 times concordantly or discordantly; of these: 7300836 mates make up the pairs; of these: 4516467 (61.86%) aligned 0 times 472607 (6.47%) aligned exactly 1 time 2311762 (31.66%) aligned >1 times 91.17% overall alignment rate Time searching: 01:22:45 Overall time: 01:22:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 28 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 5552195 / 21659395 = 0.2563 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 02:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 02:06:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:06:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 02:06:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:06:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 02:06:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:06:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:06:26: 1000000 INFO @ Mon, 03 Jun 2019 02:06:26: 1000000 INFO @ Mon, 03 Jun 2019 02:06:29: 1000000 INFO @ Mon, 03 Jun 2019 02:06:38: 2000000 INFO @ Mon, 03 Jun 2019 02:06:42: 2000000 INFO @ Mon, 03 Jun 2019 02:06:43: 2000000 INFO @ Mon, 03 Jun 2019 02:06:49: 3000000 INFO @ Mon, 03 Jun 2019 02:06:57: 3000000 INFO @ Mon, 03 Jun 2019 02:06:58: 3000000 INFO @ Mon, 03 Jun 2019 02:07:01: 4000000 INFO @ Mon, 03 Jun 2019 02:07:13: 5000000 INFO @ Mon, 03 Jun 2019 02:07:14: 4000000 INFO @ Mon, 03 Jun 2019 02:07:14: 4000000 INFO @ Mon, 03 Jun 2019 02:07:25: 6000000 INFO @ Mon, 03 Jun 2019 02:07:30: 5000000 INFO @ Mon, 03 Jun 2019 02:07:31: 5000000 INFO @ Mon, 03 Jun 2019 02:07:37: 7000000 INFO @ Mon, 03 Jun 2019 02:07:47: 6000000 INFO @ Mon, 03 Jun 2019 02:07:47: 6000000 INFO @ Mon, 03 Jun 2019 02:07:49: 8000000 INFO @ Mon, 03 Jun 2019 02:08:01: 9000000 INFO @ Mon, 03 Jun 2019 02:08:02: 7000000 INFO @ Mon, 03 Jun 2019 02:08:02: 7000000 INFO @ Mon, 03 Jun 2019 02:08:13: 10000000 INFO @ Mon, 03 Jun 2019 02:08:18: 8000000 INFO @ Mon, 03 Jun 2019 02:08:18: 8000000 INFO @ Mon, 03 Jun 2019 02:08:24: 11000000 INFO @ Mon, 03 Jun 2019 02:08:32: 9000000 INFO @ Mon, 03 Jun 2019 02:08:32: 9000000 INFO @ Mon, 03 Jun 2019 02:08:35: 12000000 INFO @ Mon, 03 Jun 2019 02:08:46: 13000000 INFO @ Mon, 03 Jun 2019 02:08:47: 10000000 INFO @ Mon, 03 Jun 2019 02:08:47: 10000000 INFO @ Mon, 03 Jun 2019 02:08:59: 14000000 INFO @ Mon, 03 Jun 2019 02:09:02: 11000000 INFO @ Mon, 03 Jun 2019 02:09:04: 11000000 INFO @ Mon, 03 Jun 2019 02:09:11: 15000000 INFO @ Mon, 03 Jun 2019 02:09:19: 12000000 INFO @ Mon, 03 Jun 2019 02:09:22: 12000000 INFO @ Mon, 03 Jun 2019 02:09:22: 16000000 INFO @ Mon, 03 Jun 2019 02:09:34: 17000000 INFO @ Mon, 03 Jun 2019 02:09:37: 13000000 INFO @ Mon, 03 Jun 2019 02:09:39: 13000000 INFO @ Mon, 03 Jun 2019 02:09:45: 18000000 INFO @ Mon, 03 Jun 2019 02:09:54: 14000000 INFO @ Mon, 03 Jun 2019 02:09:56: 14000000 INFO @ Mon, 03 Jun 2019 02:09:56: 19000000 INFO @ Mon, 03 Jun 2019 02:10:07: 20000000 INFO @ Mon, 03 Jun 2019 02:10:09: 15000000 INFO @ Mon, 03 Jun 2019 02:10:11: 15000000 INFO @ Mon, 03 Jun 2019 02:10:19: 21000000 INFO @ Mon, 03 Jun 2019 02:10:25: 16000000 INFO @ Mon, 03 Jun 2019 02:10:28: 16000000 INFO @ Mon, 03 Jun 2019 02:10:29: 22000000 INFO @ Mon, 03 Jun 2019 02:10:40: 23000000 INFO @ Mon, 03 Jun 2019 02:10:42: 17000000 INFO @ Mon, 03 Jun 2019 02:10:45: 17000000 INFO @ Mon, 03 Jun 2019 02:10:50: 24000000 INFO @ Mon, 03 Jun 2019 02:10:59: 18000000 INFO @ Mon, 03 Jun 2019 02:11:01: 25000000 INFO @ Mon, 03 Jun 2019 02:11:02: 18000000 INFO @ Mon, 03 Jun 2019 02:11:11: 26000000 INFO @ Mon, 03 Jun 2019 02:11:16: 19000000 INFO @ Mon, 03 Jun 2019 02:11:19: 19000000 INFO @ Mon, 03 Jun 2019 02:11:21: 27000000 INFO @ Mon, 03 Jun 2019 02:11:32: 28000000 INFO @ Mon, 03 Jun 2019 02:11:33: 20000000 INFO @ Mon, 03 Jun 2019 02:11:35: 20000000 INFO @ Mon, 03 Jun 2019 02:11:42: 29000000 INFO @ Mon, 03 Jun 2019 02:11:49: 21000000 INFO @ Mon, 03 Jun 2019 02:11:52: 21000000 INFO @ Mon, 03 Jun 2019 02:11:53: 30000000 INFO @ Mon, 03 Jun 2019 02:12:04: 31000000 INFO @ Mon, 03 Jun 2019 02:12:05: 22000000 INFO @ Mon, 03 Jun 2019 02:12:08: 22000000 INFO @ Mon, 03 Jun 2019 02:12:16: 32000000 INFO @ Mon, 03 Jun 2019 02:12:18: 23000000 INFO @ Mon, 03 Jun 2019 02:12:23: 23000000 INFO @ Mon, 03 Jun 2019 02:12:29: 33000000 INFO @ Mon, 03 Jun 2019 02:12:34: 24000000 INFO @ Mon, 03 Jun 2019 02:12:38: 24000000 INFO @ Mon, 03 Jun 2019 02:12:40: 34000000 INFO @ Mon, 03 Jun 2019 02:12:48: 25000000 INFO @ Mon, 03 Jun 2019 02:12:51: 35000000 INFO @ Mon, 03 Jun 2019 02:12:53: 25000000 INFO @ Mon, 03 Jun 2019 02:12:57: #1 tag size is determined as 121 bps INFO @ Mon, 03 Jun 2019 02:12:57: #1 tag size = 121 INFO @ Mon, 03 Jun 2019 02:12:57: #1 total tags in treatment: 14354460 INFO @ Mon, 03 Jun 2019 02:12:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:12:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:12:57: #1 tags after filtering in treatment: 10656086 INFO @ Mon, 03 Jun 2019 02:12:57: #1 Redundant rate of treatment: 0.26 INFO @ Mon, 03 Jun 2019 02:12:57: #1 finished! INFO @ Mon, 03 Jun 2019 02:12:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:12:59: #2 number of paired peaks: 3832 INFO @ Mon, 03 Jun 2019 02:12:59: start model_add_line... INFO @ Mon, 03 Jun 2019 02:12:59: start X-correlation... INFO @ Mon, 03 Jun 2019 02:12:59: end of X-cor INFO @ Mon, 03 Jun 2019 02:12:59: #2 finished! INFO @ Mon, 03 Jun 2019 02:12:59: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 02:12:59: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 02:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.20_model.r WARNING @ Mon, 03 Jun 2019 02:12:59: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:12:59: #2 You may need to consider one of the other alternative d(s): 137 WARNING @ Mon, 03 Jun 2019 02:12:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:12:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:12:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:13:02: 26000000 INFO @ Mon, 03 Jun 2019 02:13:07: 26000000 INFO @ Mon, 03 Jun 2019 02:13:16: 27000000 INFO @ Mon, 03 Jun 2019 02:13:21: 27000000 INFO @ Mon, 03 Jun 2019 02:13:30: 28000000 INFO @ Mon, 03 Jun 2019 02:13:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:13:36: 28000000 INFO @ Mon, 03 Jun 2019 02:13:45: 29000000 INFO @ Mon, 03 Jun 2019 02:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.20_summits.bed INFO @ Mon, 03 Jun 2019 02:13:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5872 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:13:51: 29000000 INFO @ Mon, 03 Jun 2019 02:14:00: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 02:14:06: 30000000 INFO @ Mon, 03 Jun 2019 02:14:15: 31000000 INFO @ Mon, 03 Jun 2019 02:14:20: 31000000 INFO @ Mon, 03 Jun 2019 02:14:28: 32000000 INFO @ Mon, 03 Jun 2019 02:14:32: 32000000 INFO @ Mon, 03 Jun 2019 02:14:44: 33000000 INFO @ Mon, 03 Jun 2019 02:14:48: 33000000 INFO @ Mon, 03 Jun 2019 02:14:59: 34000000 INFO @ Mon, 03 Jun 2019 02:15:02: 34000000 BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 02:15:14: 35000000 INFO @ Mon, 03 Jun 2019 02:15:17: 35000000 INFO @ Mon, 03 Jun 2019 02:15:21: #1 tag size is determined as 121 bps INFO @ Mon, 03 Jun 2019 02:15:21: #1 tag size = 121 INFO @ Mon, 03 Jun 2019 02:15:21: #1 total tags in treatment: 14354460 INFO @ Mon, 03 Jun 2019 02:15:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:15:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:15:22: #1 tags after filtering in treatment: 10656086 INFO @ Mon, 03 Jun 2019 02:15:22: #1 Redundant rate of treatment: 0.26 INFO @ Mon, 03 Jun 2019 02:15:22: #1 finished! INFO @ Mon, 03 Jun 2019 02:15:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:15:23: #2 number of paired peaks: 3832 INFO @ Mon, 03 Jun 2019 02:15:23: start model_add_line... INFO @ Mon, 03 Jun 2019 02:15:23: start X-correlation... INFO @ Mon, 03 Jun 2019 02:15:23: end of X-cor INFO @ Mon, 03 Jun 2019 02:15:23: #2 finished! INFO @ Mon, 03 Jun 2019 02:15:23: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 02:15:23: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 02:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.05_model.r WARNING @ Mon, 03 Jun 2019 02:15:23: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:15:23: #2 You may need to consider one of the other alternative d(s): 137 WARNING @ Mon, 03 Jun 2019 02:15:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:15:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:15:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:15:24: #1 tag size is determined as 121 bps INFO @ Mon, 03 Jun 2019 02:15:24: #1 tag size = 121 INFO @ Mon, 03 Jun 2019 02:15:24: #1 total tags in treatment: 14354460 INFO @ Mon, 03 Jun 2019 02:15:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:15:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:15:24: #1 tags after filtering in treatment: 10656086 INFO @ Mon, 03 Jun 2019 02:15:24: #1 Redundant rate of treatment: 0.26 INFO @ Mon, 03 Jun 2019 02:15:24: #1 finished! INFO @ Mon, 03 Jun 2019 02:15:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:15:26: #2 number of paired peaks: 3832 INFO @ Mon, 03 Jun 2019 02:15:26: start model_add_line... INFO @ Mon, 03 Jun 2019 02:15:26: start X-correlation... INFO @ Mon, 03 Jun 2019 02:15:26: end of X-cor INFO @ Mon, 03 Jun 2019 02:15:26: #2 finished! INFO @ Mon, 03 Jun 2019 02:15:26: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 02:15:26: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 02:15:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.10_model.r WARNING @ Mon, 03 Jun 2019 02:15:26: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:15:26: #2 You may need to consider one of the other alternative d(s): 137 WARNING @ Mon, 03 Jun 2019 02:15:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:15:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:15:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:15:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:15:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:16:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:16:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:16:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.05_summits.bed INFO @ Mon, 03 Jun 2019 02:16:11: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (12787 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:16:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2145596/ERX2145596.10_summits.bed INFO @ Mon, 03 Jun 2019 02:16:14: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9620 records, 4 fields): 15 millis CompletedMACS2peakCalling